Browse by volume Browse by section Browse by topic Browse by conference

Section: Mathematical & Computational Biology
Topic: Agricultural sciences, Ecology, Computer sciences

A workflow for processing global datasets: application to intercropping

Mahmoud, Rémi1 ; Casadebaig, Pierre1 ; Hilgert, Nadine2 ; Gaudio, Noémie1
1 AGIR, Univ. Toulouse, INRAE, Castanet-Tolosan, France
2 MISTEA, Univ. Montpellier, INRAE, Institut Agro, Montpellier, France

10.24072/pcjournal.389 - Peer Community Journal, Volume 4 (2024), article no. e24.

Get full text PDF Peer reviewed and recommended by PCI

Field experiments are a key source of data and knowledge in agricultural research. An emerging practice is to compile the measurements and results of these experiments (rather than the results of publications, as in meta-analysis) into global datasets. Our aim in the present study was to provide several methodological paths related to the design of global datasets. We considered 37 field experiments as the use case for designing a global dataset and illustrated how tidying and disseminating the data are the first steps towards open science practices. We developed a method to identify complete factorial designs within global datasets using tools from graph theory. We discuss the position of global datasets in the continuum between data and knowledge, compared to other approaches such as meta-analysis. We advocate using global datasets more widely in agricultural research.

Published online:
DOI: 10.24072/pcjournal.389
Type: Research article
Mahmoud, Rémi 1; Casadebaig, Pierre 1; Hilgert, Nadine 2; Gaudio, Noémie 1

1 AGIR, Univ. Toulouse, INRAE, Castanet-Tolosan, France
2 MISTEA, Univ. Montpellier, INRAE, Institut Agro, Montpellier, France
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights 
@article{10_24072_pcjournal_389,
     author = {Mahmoud, R\'emi and Casadebaig, Pierre and Hilgert, Nadine and Gaudio, No\'emie},
     title = {A workflow for processing global datasets: application to intercropping},
     journal = {Peer Community Journal},
     eid = {e24},
     publisher = {Peer Community In},
     volume = {4},
     year = {2024},
     doi = {10.24072/pcjournal.389},
     language = {en},
     url = {https://peercommunityjournal.org/articles/10.24072/pcjournal.389/}
}
TY  - JOUR
AU  - Mahmoud, Rémi
AU  - Casadebaig, Pierre
AU  - Hilgert, Nadine
AU  - Gaudio, Noémie
TI  - A workflow for processing global datasets: application to intercropping
JO  - Peer Community Journal
PY  - 2024
VL  - 4
PB  - Peer Community In
UR  - https://peercommunityjournal.org/articles/10.24072/pcjournal.389/
DO  - 10.24072/pcjournal.389
LA  - en
ID  - 10_24072_pcjournal_389
ER  - 
%0 Journal Article
%A Mahmoud, Rémi
%A Casadebaig, Pierre
%A Hilgert, Nadine
%A Gaudio, Noémie
%T A workflow for processing global datasets: application to intercropping
%J Peer Community Journal
%D 2024
%V 4
%I Peer Community In
%U https://peercommunityjournal.org/articles/10.24072/pcjournal.389/
%R 10.24072/pcjournal.389
%G en
%F 10_24072_pcjournal_389
Mahmoud, Rémi; Casadebaig, Pierre; Hilgert, Nadine; Gaudio, Noémie. A workflow for processing global datasets: application to intercropping. Peer Community Journal, Volume 4 (2024), article  no. e24. doi : 10.24072/pcjournal.389. https://peercommunityjournal.org/articles/10.24072/pcjournal.389/

PCI peer reviews and recommendation, and links to data, scripts, code and supplementary information: 10.24072/pci.mcb.100197

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

[1] Ackoff, R. L. From data to wisdom, Journal of applied systems analysis, Volume 16 (1989) no. 1, pp. 3-9

[2] Allen, I. E.; Olkin, I. Estimating Time to Conduct a Meta-analysis From Number of Citations Retrieved, JAMA: The Journal of the American Medical Association, Volume 282 (1999) no. 7, pp. 634-635 | DOI

[3] Barillot, R.; Combes, D.; Pineau, S.; Huynh, P.; Escobar-Gutiérrez, A. J. Comparison of the morphogenesis of three genotypes of pea (Pisum sativum) grown in pure stands and wheat-based intercrops, AoB PLANTS, Volume 6 (2014) | DOI

[4] Bedoussac, L.; Justes, E. Dynamic analysis of competition and complementarity for light and N use to understand the yield and the protein content of a durum wheat–winter pea intercrop, Plant and Soil, Volume 330 (2010) no. 1-2, pp. 37-54 | DOI

[5] Bedoussac, L.; Justes, E. The efficiency of a durum wheat-winter pea intercrop to improve yield and wheat grain protein concentration depends on N availability during early growth, Plant and Soil, Volume 330 (2010) no. 1-2, pp. 19-35 | DOI

[6] Berghuijs, H. N.; Weih, M.; van der Werf, W.; Karley, A. J.; Adam, E.; Villegas-Fernández, Á. M.; Kiær, L. P.; Newton, A. C.; Scherber, C.; Tavoletti, S.; Vico, G. Calibrating and testing APSIM for wheat-faba bean pure cultures and intercrops across Europe, Field Crops Research, Volume 264 (2021) | DOI

[7] Broman, K. W.; Woo, K. H. Data Organization in Spreadsheets, The American Statistician, Volume 72 (2018) no. 1, pp. 2-10 | DOI

[8] Bron, C.; Kerbosch, J. Algorithm 457: Finding All Cliques of an Undirected Graph [H], Communications of the ACM, Volume 16 (1973) no. 9, pp. 575-577 | DOI

[9] Casler, M. D. Fundamentals of Experimental Design: Guidelines for Designing Successful Experiments, Agronomy Journal, Volume 107 (2015) no. 2, pp. 692-705 | DOI

[10] Corre-Hellou, G.; Fustec, J.; Crozat, Y. Interspecific competition for soil N and its interaction with N-2 fixation, leaf expansion and crop growth in pea-barley intercrops, Plant and Soil, Volume 282 (2006) no. 1-2, pp. 195-208 | DOI

[11] Cruz, S. M. S. d.; Nascimento, J. A. P. d. Towards integration of data-driven agronomic experiments with data provenance, Computers and Electronics in Agriculture, Volume 161 (2019), pp. 14-28 | DOI

[12] Duru, M.; Therond, O.; Martin, G.; Martin-Clouaire, R.; Magne, M.-A.; Justes, E.; Journet, E.-P.; Aubertot, J.-N.; Savary, S.; Bergez, J.-E.; Sarthou, J. P. How to implement biodiversity-based agriculture to enhance ecosystem services: a review, Agronomy for Sustainable Development, Volume 35 (2015) no. 4, pp. 1259-1281 | DOI

[13] Garside, A. L.; Bell, M. J. Growth and yield responses to amendments to the sugarcane monoculture: Towards identifying the reasons behind the response to breaks, Crop and Pasture Science, Volume 62 (2011) no. 9, pp. 776-789 | DOI

[14] Gaudio, N.; Mahmoud, R.; Bedoussac, L.; Justes, E.; Journet, E.-P.; Naudin, C.; Hauggaard-Nielsen, H.; Jensen, E. S.; Pelzer, E.; Corre-Hellou, G.; Kammoun, B.; Viguier, L.; Barillot, R.; Couëdel, A.; Hinsinger, P.; Casadebaig, P. A global dataset gathering 37 field experiments involving cereal-legume intercrops and their corresponding sole crops., Zenodo, 2023 | DOI

[15] Gaudio, N.; Violle, C.; Gendre, X.; Fort, F.; Mahmoud, R.; Pelzer, E.; Médiène, S.; Hauggaard-Nielsen, H.; Bedoussac, L.; Bonnet, C.; Corre-Hellou, G.; Couëdel, A.; Hinsinger, P.; Jensen, E. S.; Journet, E.-P.; Justes, E.; Kammoun, B.; Litrico, I.; Moutier, N.; Naudin, C.; Casadebaig, P. Interspecific interactions regulate plant reproductive allometry in cereal–legume intercropping systems, Journal of Applied Ecology, Volume 58 (2021) no. 11, pp. 2579-2589 | DOI

[16] Glass, G. Primary, secondary, and meta-analysis of research, Educational researcher, Volume 5 (1976), pp. 3-8

[17] Gunawardena, J. Models in biology: ‘accurate descriptions of our pathetic thinking’, BMC Biology, Volume 12 (2014) no. 1 | DOI

[18] Hauggaard-Nielsen, H.; Gooding, M.; Ambus, P.; Corre-Hellou, G.; Crozat, Y.; Dahlmann, C.; Dahlmann, C.; Fragstein, P. v.; Pristeri, A.; Monti, M.; Jensen, E. S. Pea-barley intercropping for efficient symbiotic N-2-fixation, soil N acquisition and use of other nutrients in European organic cropping systems, Field Crops Research, Volume 113 (2009) no. 1, pp. 64-71 | DOI

[19] Hauggaard-Nielsen, H.; Gooding, M.; Ambus, P.; Corre-Hellou, G.; Crozat, Y.; Dahlmann, C.; Dibet, A.; von Fragstein, P.; Pristeri, A.; Monti, M.; Jensen, E. S. Pea-barley intercropping and short-term subsequent crop effects across European organic cropping conditions, Nutrient Cycling in Agroecosystems, Volume 85 (2009) no. 2, pp. 141-155 | DOI

[20] Hauggaard-Nielsen, H.; Jørnsgaard, B.; Kinane, J.; Jensen, E. S. Grain legume–cereal intercropping: The practical application of diversity, competition and facilitation in arable and organic cropping systems, Renewable Agriculture and Food Systems, Volume 23 (2008) no. 1, pp. 3-12 (Publisher: Cambridge University Press) | DOI

[21] Jenkins, G. B.; Beckerman, A. P.; Bellard, C.; Benítez‐López, A.; Ellison, A. M.; Foote, C. G.; Hufton, A. L.; Lashley, M. A.; Lortie, C. J.; Ma, Z.; Moore, A. J.; Narum, S. R.; Nilsson, J.; O'Boyle, B.; Provete, D. B.; Razgour, O.; Rieseberg, L.; Riginos, C.; Santini, L.; Sibbett, B.; Peres‐Neto, P. R. Reproducibility in ecology and evolution: Minimum standards for data and code, Ecology and Evolution, Volume 13 (2023) no. 5 | DOI

[22] Kammoun, B.; Journet, E.-P.; Justes, E.; Bedoussac, L. Cultivar Grain Yield in Durum Wheat-Grain Legume Intercrops Could Be Estimated From Sole Crop Yields and Interspecific Interaction Index, Frontiers in Plant Science, Volume 12 (2021), p. 2191 | DOI

[23] Kattge, J.; Díaz, S.; Lavorel, S.; Prentice, I. C.; Leadley, P.; Bönisch, G.; Garnier, E.; Westoby, M.; Reich, P. B.; Wright, I. J.; Cornelissen, J. H. C.; Violle, C.; Harrison, S. P.; Van Bodegom, P. M.; Reichstein, M.; Enquist, B. J.; Soudzilovskaia, N. A.; Ackerly, D. D.; Anand, M.; Atkin, O.; Bahn, M.; Baker, T. R.; Baldocchi, D.; Bekker, R.; Blanco, C. C.; Blonder, B.; Bond, W. J.; Bradstock, R.; Bunker, D. E.; Casanoves, F.; Cavender‐Bares, J.; Chambers, J. Q.; Chapin Iii, F. S.; Chave, J.; Coomes, D.; Cornwell, W. K.; Craine, J. M.; Dobrin, B. H.; Duarte, L.; Durka, W.; Elser, J.; Esser, G.; Estiarte, M.; Fagan, W. F.; Fang, J.; Fernández‐Méndez, F.; Fidelis, A.; Finegan, B.; Flores, O.; Ford, H.; Frank, D.; Freschet, G. T.; Fyllas, N. M.; Gallagher, R. V.; Green, W. A.; Gutierrez, A. G.; Hickler, T.; Higgins, S. I.; Hodgson, J. G.; Jalili, A.; Jansen, S.; Joly, C. A.; Kerkhoff, A. J.; Kirkup, D.; Kitajima, K.; Kleyer, M.; Klotz, S.; Knops, J. M. H.; Kramer, K.; Kühn, I.; Kurokawa, H.; Laughlin, D.; Lee, T. D.; Leishman, M.; Lens, F.; Lenz, T.; Lewis, S. L.; Lloyd, J.; Llusià, J.; Louault, F.; Ma, S.; Mahecha, M. D.; Manning, P.; Massad, T.; Medlyn, B. E.; Messier, J.; Moles, A. T.; Müller, S. C.; Nadrowski, K.; Naeem, S.; Niinemets, Ü.; Nöllert, S.; Nüske, A.; Ogaya, R.; Oleksyn, J.; Onipchenko, V. G.; Onoda, Y.; Ordoñez, J.; Overbeck, G.; Ozinga, W. A.; Patiño, S.; Paula, S.; Pausas, J. G.; Peñuelas, J.; Phillips, O. L.; Pillar, V.; Poorter, H.; Poorter, L.; Poschlod, P.; Prinzing, A.; Proulx, R.; Rammig, A.; Reinsch, S.; Reu, B.; Sack, L.; Salgado‐Negret, B.; Sardans, J.; Shiodera, S.; Shipley, B.; Siefert, A.; Sosinski, E.; Soussana, J.; Swaine, E.; Swenson, N.; Thompson, K.; Thornton, P.; Waldram, M.; Weiher, E.; White, M.; White, S.; Wright, S. J.; Yguel, B.; Zaehle, S.; Zanne, A. E.; Wirth, C. TRY – a global database of plant traits, Global Change Biology, Volume 17 (2011) no. 9, pp. 2905-2935 | DOI

[24] Knudsen, M. T.; Hauggaard-Nielsen, H.; Jornsgard, B.; Jensen, E. S. Comparison of interspecific competition and N use in pea-barley, faba bean-barley and lupin-barley intercrops grown at two temperate locations, Journal of Agricultural Science, Volume 142 (2004), pp. 617-627 | DOI

[25] Krajewski, P.; Chen, D.; Ćwiek, H.; van Dijk, A. D. J.; Fiorani, F.; Kersey, P.; Klukas, C.; Lange, M.; Markiewicz, A.; Nap, J. P.; van Oeveren, J.; Pommier, C.; Scholz, U.; van Schriek, M.; Usadel, B.; Weise, S. Towards recommendations for metadata and data handling in plant phenotyping, Journal of Experimental Botany, Volume 66 (2015) no. 18, pp. 5417-5427 | DOI

[26] Launay, M.; Brisson, N.; Satger, S.; Hauggaard-Nielsen, H.; Corre-Hellou, G.; Kasynova, E.; Ruske, R.; Jensen, E. S.; Gooding, M. J. Exploring options for managing strategies for pea-barley intercropping using a modeling approach, European Journal of Agronomy, Volume 31 (2009) no. 2, pp. 85-98 | DOI

[27] Lawler, E. L.; Lenstra, J. K.; Rinnooy Kan, A. H. G. Generating All Maximal Independent Sets: NP-Hardness and Polynomial-Time Algorithms, SIAM Journal on Computing, Volume 9 (1980) no. 3, pp. 558-565 | DOI

[28] Licker, R.; Johnston, M.; Foley, J. A.; Barford, C.; Kucharik, C. J.; Monfreda, C.; Ramankutty, N. Mind the gap: How do climate and agricultural management explain the 'yield gap' of croplands around the world?, Global Ecology and Biogeography, Volume 19 (2010) no. 6, pp. 769-782 | DOI

[29] Lobell, D. B.; Deines, J. M.; Tommaso, S. D. Changes in the drought sensitivity of US maize yields, Nature Food, Volume 1 (2020) no. 11, pp. 729-735 | DOI

[30] Louarn, G.; Barillot, R.; Combes, D.; Escobar-Gutiérrez, A. Towards intercrop ideotypes: Non-random trait assembly can promote overyielding and stability of species proportion in simulated legume-based mixtures, Annals of Botany, Volume 126 (2020) no. 4, pp. 671-685 | DOI

[31] Louarn, G.; Bedoussac, L.; Gaudio, N.; Journet, E. P.; Moreau, D.; Steen Jensen, E.; Justes, E. Plant nitrogen nutrition status in intercrops– a review of concepts and methods, European Journal of Agronomy, Volume 124 (2021), p. 126229 | DOI

[32] Lowndes, J. S. S.; Best, B. D.; Scarborough, C.; Afflerbach, J. C.; Frazier, M. R.; O’Hara, C. C.; Jiang, N.; Halpern, B. S. Our path to better science in less time using open data science tools, Nature Ecology & Evolution, Volume 1 (2017) no. 6, pp. 1-7 (Number: 6 Publisher: Nature Publishing Group) | DOI

[33] Maat, H. The history and future of agricultural experiments, NJAS: Wageningen Journal of Life Sciences, Volume 57 (2011) no. 3-4, pp. 187-195 | DOI

[34] Mahmoud, R.; Casadebaig, P.; Hilgert, N.; Alletto, L.; Freschet, G. T.; de Mazancourt, C.; Gaudio, N. Species choice and N fertilization influence yield gains through complementarity and selection effects in cereal-legume intercrops, Agronomy for Sustainable Development, Volume 42 (2022) no. 2 | DOI

[35] Makowski, D.; Nesme, T.; Papy, F.; Doré, T. Global agronomy, a new field of research. A review, Agronomy for Sustainable Development, Volume 34 (2014) no. 2, pp. 293-307 | DOI

[36] Meunier, C.; Alletto, L.; Bedoussac, L.; Bergez, J.-E.; Casadebaig, P.; Constantin, J.; Gaudio, N.; Mahmoud, R.; Aubertot, J.-N.; Celette, F.; Guinet, M.; Jeuffroy, M.-H.; Robin, M.-H.; Médiène, S.; Fontaine, L.; Nicolardot, B.; Pelzer, E.; Souchère, V.; Voisin, A.-S.; Rosiès, B.; Casagrande, M.; Martin, G. A modelling chain combining soft and hard models to assess a bundle of ecosystem services provided by a diversity of cereal-legume intercrops, European Journal of Agronomy, Volume 132 (2022) | DOI

[37] Naudin, C.; Corre-Hellou, G.; Pineau, S.; Crozat, Y.; Jeuffroy, M.-H. The effect of various dynamics of N availability on winter pea-wheat intercrops: Crop growth, N partitioning and symbiotic N-2 fixation, Field Crops Research, Volume 119 (2010) no. 1, pp. 2-11 | DOI

[38] Naudin, C.; van der Werf, H. M. G.; Jeuffroy, M.-H.; Corre-Hellou, G. Life cycle assessment applied to pea-wheat intercrops: A new method for handling the impacts of co-products, Journal of Cleaner Production, Volume 73 (2014), pp. 80-87 | DOI

[39] Newman, S. J.; Furbank, R. T. A multiple species, continent-wide, million-phenotype agronomic plant dataset, Scientific Data, Volume 8 (2021) no. 1, pp. 1-8 | DOI

[40] Pelzer, E.; Bazot, M.; Guichard, L.; Jeuffroy, M.-H. Crop Management Affects the Performance of a Winter Pea–Wheat Intercrop, Agronomy Journal, Volume 108 (2016) no. 3, pp. 1089-1100 | DOI

[41] Phillips, C. A.; Wang, K.; Baker, E. J.; Bubier, J. A.; Chesler, E. J.; Langston, M. A. On Finding and enumerating maximal and maximum k-partite cliques in k-partite graphs, Algorithms, Volume 12 (2019) no. 1 | DOI

[42] Popkin, G. Data sharing and how it can benefit your scientific career, Nature, Volume 569 (2019) no. 7756, pp. 445-447 | DOI

[43] Senft, M.; Stahl, U.; Svoboda, N. Research data management in agricultural sciences in Germany: We are not yet where we want to be, PLOS ONE, Volume 17 (2022) no. 9 | DOI

[44] Sparks, A. H. nasapower: A NASA POWER Global Meteorology, Surface Solar Energy and Climatology Data Client for R, Journal of Open Source Software, Volume 3 (2018) no. 30, p. 1035 | DOI

[45] Tang, X.; Placella, S. A.; Dayde, F.; Bernard, L.; Robin, A.; Journet, E.-P.; Justes, E.; Hinsinger, P. Phosphorus availability and microbial community in the rhizosphere of intercropped cereal and legume along a P-fertilizer gradient, Plant and Soil, Volume 407 (2016) no. 1-2, pp. 119-134 | DOI

[46] Tannier, E. Collecting, assembling and sharing data in crop sciences, Peer Community in Mathematical and Computational Biology (2024) | DOI

[47] Tardieu, F. Educated big data to study sensitivity to drought, Nature Food, Volume 1 (2020) no. 11, pp. 669-670 | DOI

[48] Viguier, L.; Bedoussac, L.; Journet, E.-P.; Justes, E. Yield gap analysis extended to marketable grain reveals the profitability of organic lentil-spring wheat intercrops, Agronomy for Sustainable Development, Volume 38 (2018) no. 4, p. 39 | DOI

[49] White, J. W.; Van Evert, F. K. Publishing agronomic data, Agronomy Journal, Volume 100 (2008) no. 5, pp. 1396-1400 | DOI

[50] Wickham, H.; Grolemund, G. R for data science: import, tidy, transform, visualize, and model data, O'Reilly Media, Inc., 2016 (https://r4ds.had.co.nz/)

[51] Wilkinson, M. D.; Dumontier, M.; Aalbersberg, I. J.; Appleton, G.; Axton, M.; Baak, A.; Blomberg, N.; Boiten, J. W.; da Silva Santos, L. B.; Bourne, P. E.; Bouwman, J.; Brookes, A. J.; Clark, T.; Crosas, M.; Dillo, I.; Dumon, O.; Edmunds, S.; Evelo, C. T.; Finkers, R.; Gonzalez-Beltran, A.; Gray, A. J.; Groth, P.; Goble, C.; Grethe, J. S.; Heringa, J.; t Hoen, P. A.; Hooft, R.; Kuhn, T.; Kok, R.; Kok, J.; Lusher, S. J.; Martone, M. E.; Mons, A.; Packer, A. L.; Persson, B.; Rocca-Serra, P.; Roos, M.; van Schaik, R.; Sansone, S. A.; Schultes, E.; Sengstag, T.; Slater, T.; Strawn, G.; Swertz, M. A.; Thompson, M.; Van Der Lei, J.; Van Mulligen, E.; Velterop, J.; Waagmeester, A.; Wittenburg, P.; Wolstencroft, K.; Zhao, J.; Mons, B. Comment: The FAIR Guiding Principles for scientific data management and stewardship, Scientific Data, Volume 3 (2016), pp. 1-9 | DOI

[52] Wilson, G.; Bryan, J.; Cranston, K.; Kitzes, J.; Nederbragt, L.; Teal, T. K. Good enough practices in scientific computing, PLOS Computational Biology, Volume 13 (2017) no. 6, p. e1005510 | DOI

[53] Zamir, D. Where Have All the Crop Phenotypes Gone?, PLoS Biology, Volume 11 (2013) no. 6, pp. 1-4 | DOI

Cited by Sources: